Astrogator's Logs

GFAJ-1 is an arsenate-resistant, phosphate-dependent organism — title of the paper by Erb et al, Science, July 2012

Everyone will recall the hype and theatrical gyrations which accompanied NASA’s announcement in December 2010 that scientists funded by NASA astrobiology grants had “discovered alien life” – later modified to “alternative terrestrial biochemistry” which somehow seemed tailor-made to prove the hypothesis of honorary co-author Paul Davies about life originating from a “shadow biosphere”.

As I discussed in The Agency that Cried “Awesome!, the major problem was not the claim per se but the manner in which it was presented by Science and NASA and the behavior of its originators. It was an astonishing case of serial failure at every single level of the process: the primary researcher, the senior supervisor, the reviewers, the journal, the agency. The putative and since disproved FTL neutrinos stand as an interesting contrast: in that case, the OPERA team announced it to the community as a puzzle, and asked everyone who was willing and able to pick their results apart and find whatever error might be lurking in their methods of observation or analysis.

Those of us who are familiar with bacteria and molecular/cellular biology techniques knew instantly upon reading the original “arsenic life” paper that it was so shoddy that it should never have been published, let alone in a top-ranking journal like Science: controls were lacking or sloppy, experiments crucial for buttressing the paper’s conclusions were missing, while other results contradicted the conclusions stated by the authors. It was plain that what the group had discovered and cultivated were extremophilic bacteria that were able to tolerate high arsenic concentrations but still needed phosphorus to grow and divide.

The paper’s authors declined to respond to any but “peer-reviewed” rebuttals. A first round of eight such rebuttals, covering the multiple deficiencies of the work, accompanied its appearance in the print version of Science (a very unusual step for a journal). Still not good enough for the original group: now only replication of the entire work would do. Of course, nobody wants to spend time and precious funds replicating what they consider worthless. Nevertheless, two groups finally got exasperated enough to do exactly that, except they also performed the crucial experiments missing in the original paper: for example, spectrometry to discover if arsenic is covalently bound to any of the bacterium’s biomolecules and rigorous quantification of the amount of phosphorus present in the feeding media. The salient results from both studies, briefly:

— The bacteria do not grow if phosphorus is rigorously excluded;
— There is no covalently bound arsenic in their DNA;
— There is a tiny amount of arsenic in their sugars, but this happens abiotically.

The totality of the results suggests that GFAJ-1 bacteria have found a way to sequester toxic arsenic (already indicated by their appearance) and to preferentially ingest and utilize the scant available phosphorus. I suspect that future work on them will show that they have specialized repair enzymes and ion pumps. This makes the strain as interesting as other exotic extremophiles – no less, but certainly no more.

What has been the response of the people directly involved? Here’s a sample:

Felisa Wolfe-Simon, first author of the “arsenic-life” paper: “There is nothing in the data of these new papers that contradicts our published data.”

Ronald Oremland, Felisa Wolfe-Simon’s supervisor for the GFAJ-1 work: “… at this point I would say it [the door of “arsenic based” life] is still just a tad ajar, with points worthy of further study before either slamming it shut or opening it further and allowing more knowledge to pass through.”

John Tainer, Felisa Wolfe-Simon’s current supervisor: “There are many reasons not to find things — I don’t find my keys some mornings. That doesn’t mean they don’t exist.”

Michael New, astrobiologist, NASA headquarters: “Though these new papers challenge some of the conclusions of the original paper, neither paper invalidates the 2010 observations of a remarkable micro-organism.”

At least Science made a cautious stab at reality in its editorial, although it should have spared everyone — the original researchers included — by retracting the paper and marking it as retracted for future reference. The responses are so contrary to fact and correct scientific practice (though familiar to politician-watchers) that I am forced to conclude that perhaps the OPERA neutrino results were true after all, and I live in a universe in which it is possible to change the past via time travel.

Science is an asymptotic approach to truth; but to reach that truth, we must let go of hypotheses in which we may have become emotionally vested. That is probably the hardest internal obstacle to doing good science. The attachment to a hypothesis, coupled with the relentless pressure to be first, original, paradigm-shifting can lead to all kinds of dangerous practices – from cutting corners and omitting results that “don’t fit” to outright fraud. This is particularly dangerous when it happens to senior scientists with clout and reputations, who can flatten rivals and who often have direct access to pop media. The result is shoddy science and a disproportionate decrease of scientists’ credibility with the lay public.

The two latest papers have done far more than “challenge” the original findings. Sagan may have said that “Absence of evidence is not evidence of absence,” but he also explained how persistent lack of evidence after attempts from all angles must eventually lead to the acceptance that there is no dragon in that garage, no unicorn in that secret glade, no extant alternative terrestrial biochemistry, only infinite variations at its various scales. It’s time to put “arsenic-based life” in the same attic box that holds ether, Aristotle’s homunculi, cold fusion, FTL neutrinos, tumors dissolved by prayer. The case is obviously still open for alternative biochemistry beyond our planet and for alternative early forms on earth that went extinct without leaving traces.

We scientists have a ton of real work to do without wasting our pitifully small and constantly dwindling resources and without muddying the waters with refuse. Being human, we cannot help but occasionally fall in love with our hypotheses. But we have to take that bitter reality medicine and keep on exploring; the universe doesn’t care what we like but still has wonders waiting to be discovered. I hope that Felisa Wolfe-Simon remains one of the astrogators, as long as she realizes that following a star is not the same as following a will-o’-the-wisp — and that knowingly and willfully following the latter endangers the starship and its crew.

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15 Responses to ““Arsenic” Life or: There Is TOO a Dragon in My Garage!”

Reading this reminds me of the many researchers who claimed to see canals on Mars, walled cities on the Moon (supposedly built by giants!!), and other such exotica. The pressure to be first and the desire to discover exciting things leads scientists to see only what they want to see. This is not good science.

Perhaps we lived in a wonderful parallel Earth with rocket ships, time travel, and honest scientists until some foolish time tourist stepped on a butterfly while hunting dinosaurs- and now look where we are!! (cue an ominous sound of thunder in the distance)http://www.youtube.com/watch?v=wkLT57mVnGE&feature=relmfu

Not a bad analogy; even during the height of the “canals” craze it was obvious that they tended to “appear” when someone used low-resolution telescopes. Refusing to recognize potential artifacts is a common sign of having fallen in love with one’s hypothesis. There is a remedy for this: using alternative techniques for independent confirmation. In the case of GFAJ-1, there is a simple, traditional technique for the DNA portion which I discussed in The Agency that Cried Awesome! — namely, a cesium chloride gradient. The “arsenic life” group either didn’t do it, or did it and didn’t like the results (because they didn’t fit their theory). Red flag, either case.

More like saving face, in this instance. There have been attempts to portray Felisa Wolfe-Simon as a wronged rebel hero who dared to go against the tide, resulting in her getting “evicted” from the Oremland lab and forced to go “underground”. In fact, she is currently a postdoc at the Scripps Institute, which is as mainstream and above-ground as you can get.

The common result when politics dictate science is destructive pseudoscience (see, for example, all the ACC denialism “institutes” funded by the Koch brothers and consorts).

I can imagine how this might have come to be.

NASA exec #1: “Guys, we need to do something. The latest federal budget cuts in science funding put the cards on the table. Together with the Rethuglicans’ aspirations of privatizing everything, including aerospace technoscientific programs, our future looks grim.”

#2: “We’re still something akin to a democracy. If we get the public on our side again, we might still have a future to look forward to.”

#3: “Exactly. What we need is something big. Something that screams out We Do Something Important.”

#1: “And what should that something be? The big splashes of the past were Apollo and the Shuttle. The media lost its interest in the latter after a few launches and we couldn’t even get Constellation past the PowerPoint presentation phase.”

…you’re joking, right? How are we supposed to come up with aliens if we can’t even reach farther than LEO?”

#3: “I didn’t think of physical aliens you could put in a zoo, but something tangible enough to be buzz-worthy: the strong possibility of aliens. Have our probes send anything back that could be interpreted that way?”

#1: “Let me check that. Nope.”

#2: “I thought you’ve told me we already found hints at alien life the other day?”

#1: “Oh, that. No, some of our staff work on extremophiles, bacteria that live in harsh conditions because they show what life could potentially endure.”

#3: “Hm… So, do these bugs exhibit any foreign modes of living?”

#1: “Depends on how you define ‘foreign’.”

#3: “That’s it! I can picture the headlines. ‘Aliens found living on Earth!'”

#2: “Well, that sure sounds interesting.”

#1: “Er, what?”

#3: “Could you do me a favor and send me the mail addresses of these researchers? I want to have a word with them.”

I wish I could say it was as coherent as that! I think it was more a case of people working outside their expertise who did not (want to) consult experts, coupled with desire for quick fame and the desperation that comes with dwindling resources. Now that the inevitable has happened, everyone is doing Face Saving 101. Too bad they’re so clumsy at it.

In the larger picture, there’s no question that politics- or profit-driven science is an oxymoron. See “the war on cancer” and its ilk, to say nothing of what comes out of pharma.

Today, I googled “life on Venus” just to see what came up- hoping for a discussion of microbes possibly living in Venusian clouds or just old SF stories. Instead, I found claims that a russian scientist named Leonid Ksanfomaliti has spotted evidence for extremophile lifeforms on Venus in photos sent back by the Soviet Venera probes. Here is one discussion of this sensational story.

Apparently, Leonid published a scientific paper where he questioned the idea that life can only live in Earth-like conditions. He notes that Venus has similar conditions to the many “hot Jupiter” exoplanets that have been discovered lately, and says that if we hypothesize that life may exist under the extreme conditions that exist under such extreme conditions, we should not assume that Venus lacks life. Therefore he has examined data from the successful Venera probes in search of signs of life.

Leonid noted that the large landscape photos we see of Venus are in fact mosaics composed of the best parts of many separate photos. He examined each panorama separately and searched for changes. Then he said we can attempt to determine if these changes are abiotic in origin or are caused by the hypothetical Venusian organisms. The problem is that these images have lots of noise, and apparently were also sharpened and processed in Microsoft Windows Paint, so there isn’t any point in analyzing ever single little blobby artifact and claim it is a Venusian scorpion or shell. But that is exactly what Leonid does. It reminds me of UFO believers who see glass obelisks in pictures of the Moon and pyramids on Mars.

I don’t have a problem with questioning the idea that alien life must live on a planet with Earth-like conditions, but any hypothesis must have evidence in its favor that can’t be explained by a discarded lens cap and image artifacts. Especially the crazy, off-the-wall hypotheses. If there are indeed Venusian “scorpions” and “crabs” crawling around the Venera probes, we’ll have to wait for another Venus probe to spot them. Until then, there doesn’t seem to be any dragon in Leonid’s garage. It is a real hazard, wanting to find something so much that you see it everywhere you look…

While reading, I thought of the stir surrounding “the face on Mars” (not to mention Richard Hoagland’s claims); the efforts at face saving in the abovementioned reactions reminded of that as much as the selective theorizing of creationists.

While the methods used to support both Leonid’s theory and the “face on Mars” are similar- that is, looking at blurry enlarged photographs from space probes and seeing all sorts of fantastic things in the fuzzy, indistinct blobs- the claims themselves aren’t really that similar. The “face on Mars” people claim an advanced civilization once lived on Mars, and that these aliens left pyramids and other monuments behind. There is no evidence for the past or present existence of any sort of intelligent life on Mars, but that doesn’t stop the UFO cultists from claiming every photograph of Mars shows aliens, pyramids, and glass obelisks.

Leonid is suggesting that some exotic form of life capable of living on planets with a hot, dense poisonous atmosphere already lives on Venus. The sort of people who believe in faces on Mars think that enlightened humanoid extraterrestrials live on Venus, so I doubt they are supportive of Leonid’s hypothesis!! He’s not the first to indulge in this kind of speculation- Carl Sagan described hypothetical lifeforms that could live on Jupiter in his show Cosmos. My problem is not with the hypothesis, fantastic though it may be, but with the shaky “evidence” on which Leonid attempts to support his hypothesis.

It is difficult to imagine what an organism would have to be like to survive and thrive in Venus’s incredibly hot and dense carbon dioxide atmosphere, but life elsewhere might not follow the terrestrial pattern. I doubt that anything can live on the surface of Venus, but the idea is intriguing, especially considering all the exoplanets that probably have hot dense atmospheres like Venus. Is there some organism consistent with the known laws of physics and chemistry that could call such a planet home? Perhaps Venus would be a good place to test some of these ideas, since all the recently discovered exoplanets remain beyond our reach for now.

We have to be careful not to be too biased toward Earth life, or we might miss the presence of exotic aliens that live in an extreme environment. Even our definition of “the habitable zone” is based on the location of Earth- how do we know that aliens necessarily agree with us on what is habitable? This might even be important if humans try to terraform Venus in the far, far future- what if we began killing an entire ecosystem of strange creatures, simply because we never thought to look for them?

Using the electrical signals generated by slime mould to make music creates an instrument musicians can ‘play’ by zapping the creature with light

Physarum polycephalum, better known as slime mould, is a single-celled creature that has attracted considerable attention in recent years for its ability to compute in unconventional ways. Various research groups have watched in barely disguised amazement as these single cells have solved mazes, recreated national motorway networks and even anticipated the timing of periodic events.

Now this extraordinary creature has added another skill to its box of tricks–the ability to make music, or at least to create sound in a controlled fashion.

Physarum grows by creating a network of protoplasmic tubes that stretch from one source of food to another. Much of this creature’s computing power comes from its ability to optimise the properties of this network.

Today, Eduardo Miranda at the University of Plymouth in the UK and a couple of pals say they’ve grown a Physarum cell in a petri dish lined with six electrodes, each topped with an oat flake to attract the protoplasmic tubes.

Miranda and co then measured the electrical activity at each electrode every second as the tubes grew across them, a process that took about a week to cover all the electrodes. They then plotted the results against time to compare the activity in different electrodes.

To create a sound, Miranda and co used the signal from each electrode to control the frequency of an audio oscillator. With each electrode controlling a different range of frequencies, they then added the outputs from all the oscillators to create a complex sound that represents the activity of the Physarum.

Of course, this kind of mixing is rather arbitrary but Miranda and co are mainly interested in the sound production method. They say it is possible to control the electrical activity in different parts of the network of tubes by zapping it with light.

In a sense, this allows them to “play” the Physarum like a musical instrument.

“Our own experiments…demonstrated that varying illumination gradients are good means to tune the plasmodium to produce specific oscillatory behaviours,” they say.

They go even further in abstracting this process. “The time it takes to run experiments with Physarum polycephalum can be tedious,” they complain. So instead of growing the slime mould for real, they also simulated the process on computer to speed up the process of music making, the result being a kind of Physarum synthesiser synthesiser.

That’s certainly a bizarre form of music making but Miranda has put it to good use. Earlier this year, he premiered a piece called Die Lebensfreude in Portugal that featured the Physarum electro-acoustics.

If the goal is to push music-making beyond conventional bounds, Miranda and his colleagues must surely have succeeded. Sadly, we’re unable to judge the result since there is no link in the paper or on his website to any of the resulting sound files.